cloning_simulation: output.json comparison

comparison output.json @ 15:074a76e84b80 draft

planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

author	tduigou
date	Mon, 26 May 2025 13:39:57 +0000
parents	16ccb36aa8e3
children	fbb241adf6c2

comparison

equal deleted inserted replaced

-:16ccb36aa8e3
+:074a76e84b80
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "c173cff58a987f8f",
+"id": "1e8e6749bc68d8e8",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "genbank_files": {
-"id": "fcc5b7d13a1328f6",
+"id": "e2ca7f14a85a8d44",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/2/b/d/dataset_2bdf436f-52cc-4c6e-afdb-3f051629900f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/4/6/5/dataset_465a53ab-8770-4514-a9b3-227f79646eb7.dat,/tmp/tmpc6lic4p9/files/a/e/2/dataset_ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa.dat,/tmp/tmpc6lic4p9/files/e/6/4/dataset_e64057b1-43b3-4788-8891-77bcd297223c.dat,/tmp/tmpc6lic4p9/files/1/d/1/dataset_1d1f9832-b58e-48c2-b1b3-6c3fb18e9890.dat,/tmp/tmpc6lic4p9/files/6/7/3/dataset_6732fc79-081e-4edf-bccc-a0087520172a.dat,/tmp/tmpc6lic4p9/files/b/1/7/dataset_b17c7a49-3121-4292-95ff-51891aa066d1.dat,/tmp/tmpc6lic4p9/files/2/8/1/dataset_2811f816-8532-4ddd-8e29-9a6ed7dad54e.dat,/tmp/tmpc6lic4p9/files/e/7/4/dataset_e74d0182-807e-40a8-b67a-ac088fc2e02c.dat,/tmp/tmpc6lic4p9/files/9/d/c/dataset_9dc55c98-4ab9-4272-a680-9b3129954367.dat,/tmp/tmpc6lic4p9/files/9/5/6/dataset_95699db9-77cf-4ae1-8454-4f255f3cb62a.dat,/tmp/tmpc6lic4p9/files/1/1/9/dataset_11979c28-82ee-43c4-9e43-f34cb541f96b.dat,/tmp/tmpc6lic4p9/files/3/f/5/dataset_3f53cb86-2d2b-429a-bf51-e276bbe393fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/4/6/5/dataset_465a53ab-8770-4514-a9b3-227f79646eb7.dat:part_A.gb,/tmp/tmpc6lic4p9/files/a/e/2/dataset_ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa.dat:part_B.gb,/tmp/tmpc6lic4p9/files/e/6/4/dataset_e64057b1-43b3-4788-8891-77bcd297223c.dat:part_C.gb,/tmp/tmpc6lic4p9/files/1/d/1/dataset_1d1f9832-b58e-48c2-b1b3-6c3fb18e9890.dat:part_D.gb,/tmp/tmpc6lic4p9/files/6/7/3/dataset_6732fc79-081e-4edf-bccc-a0087520172a.dat:part_E.gb,/tmp/tmpc6lic4p9/files/b/1/7/dataset_b17c7a49-3121-4292-95ff-51891aa066d1.dat:part_F.gb,/tmp/tmpc6lic4p9/files/2/8/1/dataset_2811f816-8532-4ddd-8e29-9a6ed7dad54e.dat:part_G.gb,/tmp/tmpc6lic4p9/files/e/7/4/dataset_e74d0182-807e-40a8-b67a-ac088fc2e02c.dat:part_H.gb,/tmp/tmpc6lic4p9/files/9/d/c/dataset_9dc55c98-4ab9-4272-a680-9b3129954367.dat:part_I.gb,/tmp/tmpc6lic4p9/files/9/5/6/dataset_95699db9-77cf-4ae1-8454-4f255f3cb62a.dat:part_J.gb,/tmp/tmpc6lic4p9/files/1/1/9/dataset_11979c28-82ee-43c4-9e43-f34cb541f96b.dat:part_K.gb,/tmp/tmpc6lic4p9/files/3/f/5/dataset_3f53cb86-2d2b-429a-bf51-e276bbe393fa.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/14/outputs/dataset_ac2d98e7-ff55-4a94-9e79-861b07d63528.dat' && echo DEBUG && ls 'outdir_gb'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/2/0/d/dataset_20d4061a-81e4-4915-a841-ae8aa595c7b4.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat:part_A.gb,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat:part_B.gb,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat:part_C.gb,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat:part_D.gb,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat:part_E.gb,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat:part_G.gb,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat:part_H.gb,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat:part_I.gb,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat:part_J.gb,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat:part_K.gb,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/14/outputs/dataset_64d1d8ac-32f0-4095-be30-22eee31e24a4.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:24:01.275241",
+"create_time": "2025-05-26T12:02:32.643157",
 "dependencies": [],
 "exit_code": 0,
-"external_id": "151844",
+"external_id": "172939",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "fcc5b7d13a1328f6",
+"history_id": "e2ca7f14a85a8d44",
-"id": "c9445e550eef23d0",
+"id": "a36db940f4513bd9",
 "inputs": {
 "assembly_csv": {
-"id": "c173cff58a987f8f",
+"id": "1e8e6749bc68d8e8",
 "src": "hda",
-"uuid": "2bdf436f-52cc-4c6e-afdb-3f051629900f"
+"uuid": "20d4061a-81e4-4915-a841-ae8aa595c7b4"
 },
 "genbank_files1": {
-"id": "fcc5b7d13a1328f6",
+"id": "e2ca7f14a85a8d44",
 "src": "hda",
-"uuid": "465a53ab-8770-4514-a9b3-227f79646eb7"
+"uuid": "dd844d61-fc05-41d9-8179-21233649407d"
 },
 "genbank_files10": {
-"id": "cf75f655bb15877b",
+"id": "fbec4a551130f847",
 "src": "hda",
-"uuid": "95699db9-77cf-4ae1-8454-4f255f3cb62a"
+"uuid": "b8fd4610-2f6d-475c-8405-8bf8c2bc0306"
 },
 "genbank_files11": {
-"id": "744832bdd7ccd728",
+"id": "5bd8560352cb0b69",
 "src": "hda",
-"uuid": "11979c28-82ee-43c4-9e43-f34cb541f96b"
+"uuid": "09f4b020-4e7b-4939-b3ba-348f91cb92bc"
 },
 "genbank_files12": {
-"id": "855b83dd0dec8eab",
+"id": "cb2fe7fb50f38553",
 "src": "hda",
-"uuid": "3f53cb86-2d2b-429a-bf51-e276bbe393fa"
+"uuid": "eb730263-9442-4dca-a2dc-34b1cae450d7"
 },
 "genbank_files2": {
-"id": "df00a2d9def0cc87",
+"id": "62e98d1a229b6ef5",
 "src": "hda",
-"uuid": "ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa"
+"uuid": "cb2362f3-4b32-46cc-a227-dc15742bf9e7"
 },
 "genbank_files3": {
-"id": "d9e72a80becfe6e7",
+"id": "f8fe24202fc5b2e5",
 "src": "hda",
-"uuid": "e64057b1-43b3-4788-8891-77bcd297223c"
+"uuid": "6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a"
 },
 "genbank_files4": {
-"id": "038c626e299361e9",
+"id": "0d58e12bbe78a903",
 "src": "hda",
-"uuid": "1d1f9832-b58e-48c2-b1b3-6c3fb18e9890"
+"uuid": "33e804b2-0fbe-4844-9b5d-420e8a2db772"
 },
 "genbank_files5": {
-"id": "c7c3cd49f3337c1a",
+"id": "3937d5ff7c0e1373",
 "src": "hda",
-"uuid": "6732fc79-081e-4edf-bccc-a0087520172a"
+"uuid": "2db3825c-538b-483f-b6ff-8dc4ecc03780"
 },
 "genbank_files6": {
-"id": "51c35891e43131e2",
+"id": "473b1992d5f5b84f",
 "src": "hda",
-"uuid": "b17c7a49-3121-4292-95ff-51891aa066d1"
+"uuid": "048ee7ed-5f4c-41ef-aed4-f2cf975aac92"
 },
 "genbank_files7": {
-"id": "84db48b219855f4d",
+"id": "9b5c1fe7a52a75e0",
 "src": "hda",
-"uuid": "2811f816-8532-4ddd-8e29-9a6ed7dad54e"
+"uuid": "c505c12e-7089-4a17-a605-4f11dad6f1d7"
 },
 "genbank_files8": {
-"id": "cf00b67a5455eb5a",
+"id": "c32c50a47ebf8564",
 "src": "hda",
-"uuid": "e74d0182-807e-40a8-b67a-ac088fc2e02c"
+"uuid": "4912f12d-0842-46b7-8aaf-2a94a52f04f8"
 },
 "genbank_files9": {
-"id": "a3780ecc1a00a0d8",
+"id": "5f035ce298b798b0",
 "src": "hda",
-"uuid": "9dc55c98-4ab9-4272-a680-9b3129954367"
+"uuid": "b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "df00a2d9def0cc87",
+"id": "62e98d1a229b6ef5",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "fedb85639c7c80b9",
+"id": "182eefa577c2a56d",
 "src": "hda",
-"uuid": "4bf90377-e4de-4d13-8ebc-39a53494ea2a"
+"uuid": "991437a5-bbe4-4adb-8831-c9a871adb17f"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "bd75ec7b3d9705ea",
+"id": "979fd704a8b37879",
 "src": "hda",
-"uuid": "ac9bac0c-348b-46b7-a882-60f56867cc30"
+"uuid": "9ebdb527-8609-4bc8-85a3-f8775156c356"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "7eb30039064fccdd",
+"id": "b53ff5232a859d40",
 "src": "hda",
-"uuid": "48e39545-a44e-410b-859b-01fcf6189002"
+"uuid": "235361e4-93cc-4b56-ad81-c33ce8f593f0"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "61cc0a7b70456dfd",
+"id": "1ce0e68b6cd95b3c",
 "src": "hda",
-"uuid": "df8aca7f-8413-430f-b35f-7dac694ee0b6"
+"uuid": "49100d5c-134b-4cb0-a86b-2cf03a336b1c"
 },
 "output_zip": {
-"id": "c9445e550eef23d0",
+"id": "a36db940f4513bd9",
 "src": "hda",
-"uuid": "ac2d98e7-ff55-4a94-9e79-861b07d63528"
+"uuid": "64d1d8ac-32f0-4095-be30-22eee31e24a4"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.38it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.18it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.58it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.82it/s, now=None]\r                                                                 \r",
-"stdout": "                       1       2       3       4       5       6\n0                                                               \nconstruct_3  construct_1  part_L  part_J  part_K     NaN     NaN\nconstruct_4  construct_2  part_L  part_J  part_K     NaN     NaN\nconstruct_1       part_A  part_B  part_C  part_D  part_E  part_F\nconstruct_2       part_A  part_G  part_H  part_I  part_F     NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.38it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.18it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.58it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.82it/s, now=None]\r                                                                 \r",
-"tool_stdout": "                       1       2       3       4       5       6\n0                                                               \nconstruct_3  construct_1  part_L  part_J  part_K     NaN     NaN\nconstruct_4  construct_2  part_L  part_J  part_K     NaN     NaN\nconstruct_1       part_A  part_B  part_C  part_D  part_E  part_F\nconstruct_2       part_A  part_G  part_H  part_I  part_F     NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:24:14.526803",
+"update_time": "2025-05-26T12:02:45.106475",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 0,
-"time_seconds": 53.70547914505005,
+"time_seconds": 53.48332858085632,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-0"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "3af58a5242e85ea6",
+"id": "035124d32eef3033",
 "src": "hda"
 },
 "assembly_plan_name": "GibsonAssembly",
 "genbank_files": {
-"id": "d9e72a80becfe6e7",
+"id": "f8fe24202fc5b2e5",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/1/d/6/dataset_1d624c24-e864-463a-9fd3-0c63fd46cbd2.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/5/0/5/dataset_505aafa2-5e9c-44bb-9d26-3f3e6248fc9b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/5/0/5/dataset_505aafa2-5e9c-44bb-9d26-3f3e6248fc9b.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/17/outputs/dataset_0f617192-e625-4d9e-8358-0b9b1b0aa024.dat' && echo DEBUG && ls 'outdir_gb'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/1/6/f/dataset_16f6d475-b614-4427-9c06-95a0d56d3c92.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/17/outputs/dataset_505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:24:25.394299",
+"create_time": "2025-05-26T12:02:55.721992",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "152204",
+"external_id": "173310",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "df00a2d9def0cc87",
+"history_id": "62e98d1a229b6ef5",
-"id": "7eb30039064fccdd",
+"id": "b53ff5232a859d40",
 "inputs": {
 "assembly_csv": {
-"id": "3af58a5242e85ea6",
+"id": "035124d32eef3033",
 "src": "hda",
-"uuid": "1d624c24-e864-463a-9fd3-0c63fd46cbd2"
+"uuid": "16f6d475-b614-4427-9c06-95a0d56d3c92"
 },
 "genbank_files1": {
-"id": "3b85967b9c87a1cc",
+"id": "1fe688df02a38cc2",
 "src": "hda",
-"uuid": "505aafa2-5e9c-44bb-9d26-3f3e6248fc9b"
+"uuid": "96a8f769-3544-4407-b064-04f24a733896"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "038c626e299361e9",
+"id": "0d58e12bbe78a903",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "9773f41fb184880d",
+"id": "f970a04054a49348",
 "src": "hda",
-"uuid": "0d66c887-a6a3-4fd6-978a-9c0e2ce4b317"
+"uuid": "ff8ea1a1-10ff-4416-b944-a78a4fd3e72e"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "41b44b0c750630a6",
+"id": "ae9b306409c7f353",
 "src": "hda",
-"uuid": "be7e7183-3b0d-40dd-9908-3e8dcd7f80bf"
+"uuid": "7afee741-2c2b-4e3b-a947-819ebb5b67b4"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "bfc60c3d9bac68ee",
+"id": "791483eeafbe6bcb",
 "src": "hda",
-"uuid": "2c7f645c-33d1-4a91-9608-221494b22be4"
+"uuid": "c820ba84-23dc-4e1c-b2de-abed54b17015"
 },
 "output_zip": {
-"id": "5c8c8c874b5b07c6",
+"id": "cd80768c91dddfb6",
 "src": "hda",
-"uuid": "0f617192-e625-4d9e-8358-0b9b1b0aa024"
+"uuid": "505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"GibsonAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\rassembly:  40%|\u2588\u2588\u2588\u2588      | 2/5 [00:00<00:00,  4.24it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.27it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.28it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.48it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\rassembly:  40%|\u2588\u2588\u2588\u2588      | 2/5 [00:00<00:00,  4.35it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.33it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.53it/s, now=None]\r                                                                 \r",
-"stdout": "                  1       2       3        4        5\n0                                                    \nconstruct     parts     NaN     NaN      NaN      NaN\nconstruct_1  Frag_1  Frag_2  Frag_3   Frag_4   Frag_5\nconstruct_2  Frag_1  Frag_2  Frag_3  Frag_4b   Frag_5\nconstruct_3  Frag_1  Frag_2  Frag_3  Frag_4c  Frag_5b\nconstruct_4  Frag_1  Frag_2  Frag_3   Frag_4      NaN\nconstruct_5  Frag_1  Frag_2  Frag_3   Frag_4  Frag_4b\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\n",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\rassembly:  40%|\u2588\u2588\u2588\u2588      | 2/5 [00:00<00:00,  4.24it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.27it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.28it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.48it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/5 [00:00<?, ?it/s, now=None]\rassembly:  40%|\u2588\u2588\u2588\u2588      | 2/5 [00:00<00:00,  4.35it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.33it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.53it/s, now=None]\r                                                                 \r",
-"tool_stdout": "                  1       2       3        4        5\n0                                                    \nconstruct     parts     NaN     NaN      NaN      NaN\nconstruct_1  Frag_1  Frag_2  Frag_3   Frag_4   Frag_5\nconstruct_2  Frag_1  Frag_2  Frag_3  Frag_4b   Frag_5\nconstruct_3  Frag_1  Frag_2  Frag_3  Frag_4c  Frag_5b\nconstruct_4  Frag_1  Frag_2  Frag_3   Frag_4      NaN\nconstruct_5  Frag_1  Frag_2  Frag_3   Frag_4  Frag_4b\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\n",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:24:37.446583",
+"update_time": "2025-05-26T12:03:07.748084",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 1,
-"time_seconds": 22.626197814941406,
+"time_seconds": 22.338457345962524,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-1"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "48d1542b43af9171",
+"id": "c9169186136d0f27",
 "src": "hda"
 },
 "assembly_plan_name": "LigaseCyclingReactionAssembly",
 "genbank_files": {
-"id": "c7c3cd49f3337c1a",
+"id": "3937d5ff7c0e1373",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/a/1/f/dataset_a1f989b9-e79f-4bd7-9cf3-66675c1d1e94.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/a/6/1/dataset_a617ae1f-70e3-4873-bdcc-f2268ffeaad4.dat,/tmp/tmpc6lic4p9/files/9/4/1/dataset_941b4e95-600a-485c-a3fa-1dcf0defdd76.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/a/6/1/dataset_a617ae1f-70e3-4873-bdcc-f2268ffeaad4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpc6lic4p9/files/9/4/1/dataset_941b4e95-600a-485c-a3fa-1dcf0defdd76.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/21/outputs/dataset_827e64a1-7f84-4f9e-8468-eabb3684efa3.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/7/c/dataset_f7c9ad78-8e74-4a3c-9579-80a93ac923de.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/21/outputs/dataset_3fc625c8-722f-4efb-9c09-0d664dec2a9d.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:24:49.729783",
+"create_time": "2025-05-26T12:03:18.983816",
-"dependencies": [],
+"dependencies": [
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "flametree",
+"version": "0.1.11"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "biopython",
+"version": "1.85"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "proglog",
+"version": "0.1.10"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "pandas",
+"version": "2.2.3"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "dnacauldron",
+"version": "2.0.12"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "pdf-reports",
+"version": "0.3.9"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "sequenticon",
+"version": "0.1.8"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "dna_features_viewer",
+"version": "3.1.5"
+}
+],
 "exit_code": 0,
-"external_id": "152654",
+"external_id": "173689",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "d9e72a80becfe6e7",
+"history_id": "f8fe24202fc5b2e5",
-"id": "5c8c8c874b5b07c6",
+"id": "cd80768c91dddfb6",
 "inputs": {
 "assembly_csv": {
-"id": "48d1542b43af9171",
+"id": "c9169186136d0f27",
 "src": "hda",
-"uuid": "a1f989b9-e79f-4bd7-9cf3-66675c1d1e94"
+"uuid": "f7c9ad78-8e74-4a3c-9579-80a93ac923de"
 },
 "genbank_files1": {
-"id": "b8df5ed9fe071f18",
+"id": "f14f22136515e5fc",
 "src": "hda",
-"uuid": "a617ae1f-70e3-4873-bdcc-f2268ffeaad4"
+"uuid": "f56913bd-fc92-4122-8cf1-d9b1c60e8385"
 },
 "genbank_files2": {
-"id": "6de9142d4b5ca725",
+"id": "d00c2a698869e2f3",
 "src": "hda",
-"uuid": "941b4e95-600a-485c-a3fa-1dcf0defdd76"
+"uuid": "3b4e75b3-e6a6-459a-a959-d43ce00c3701"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "51c35891e43131e2",
+"id": "473b1992d5f5b84f",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "56521fbfdcb4ef20",
+"id": "0bb6e1adb7bbb7d6",
 "src": "hda",
-"uuid": "827e64a1-7f84-4f9e-8468-eabb3684efa3"
+"uuid": "3fc625c8-722f-4efb-9c09-0d664dec2a9d"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00,  2.16it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00,  2.40it/s, now=None]\r                                                                 \r",
-"stdout": "                                 1   ...           14\n0                                    ...             \nConstruct1         RFP_GFP_BO_10232  ...  p7_backbone\nConstruct2_flawed  RFP_GFP_BO_10232  ...          NaN\n\n[2 rows x 14 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00,  2.16it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00,  2.40it/s, now=None]\r                                                                 \r",
-"tool_stdout": "                                 1   ...           14\n0                                    ...             \nConstruct1         RFP_GFP_BO_10232  ...  p7_backbone\nConstruct2_flawed  RFP_GFP_BO_10232  ...          NaN\n\n[2 rows x 14 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:25:02.028309",
+"update_time": "2025-05-26T12:03:31.119796",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 2,
-"time_seconds": 24.395533084869385,
+"time_seconds": 23.440476655960083,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-2"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "2b17a3fa18c23b8a",
+"id": "b66a1bb5ed06a6bf",
 "src": "hda"
 },
 "assembly_plan_name": "BASICAssembly",
 "genbank_files": {
-"id": "84db48b219855f4d",
+"id": "9b5c1fe7a52a75e0",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/6/b/e/dataset_6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/c/b/a/dataset_cba9b297-4dfe-4063-8510-6c48a1b6b7a1.dat,/tmp/tmpc6lic4p9/files/3/e/8/dataset_3e8dfce1-7a05-4665-9277-388e3aa42581.dat,/tmp/tmpc6lic4p9/files/a/5/d/dataset_a5d093c2-0087-453e-b7d1-d94a7cb664e0.dat,/tmp/tmpc6lic4p9/files/0/e/c/dataset_0ec72cc0-2a95-474b-aa77-7a436dad6a9b.dat,/tmp/tmpc6lic4p9/files/d/2/7/dataset_d272199f-2e1b-49e1-a597-5ffa11507e83.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/c/b/a/dataset_cba9b297-4dfe-4063-8510-6c48a1b6b7a1.dat:GFP.gb,/tmp/tmpc6lic4p9/files/3/e/8/dataset_3e8dfce1-7a05-4665-9277-388e3aa42581.dat:p15A_kan.gb,/tmp/tmpc6lic4p9/files/a/5/d/dataset_a5d093c2-0087-453e-b7d1-d94a7cb664e0.dat:promoter.gb,/tmp/tmpc6lic4p9/files/0/e/c/dataset_0ec72cc0-2a95-474b-aa77-7a436dad6a9b.dat:RFP.gb,/tmp/tmpc6lic4p9/files/d/2/7/dataset_d272199f-2e1b-49e1-a597-5ffa11507e83.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/28/outputs/dataset_7435335e-896e-47f4-89c7-3a6c2c25f247.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/b/4/dataset_fb426ceb-2615-447d-b04e-ae4253af648d.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat:GFP.gb,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat:p15A_kan.gb,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat:promoter.gb,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat:RFP.gb,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/28/outputs/dataset_45ef7ed5-48aa-4286-ac51-3391b593eb7c.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:25:23.055332",
+"create_time": "2025-05-26T12:03:51.986652",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "153248",
+"external_id": "174270",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "038c626e299361e9",
+"history_id": "0d58e12bbe78a903",
-"id": "56521fbfdcb4ef20",
+"id": "0bb6e1adb7bbb7d6",
 "inputs": {
 "assembly_csv": {
-"id": "2b17a3fa18c23b8a",
+"id": "b66a1bb5ed06a6bf",
 "src": "hda",
-"uuid": "6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc"
+"uuid": "fb426ceb-2615-447d-b04e-ae4253af648d"
 },
 "genbank_files1": {
-"id": "aed8b1a22d89d8c9",
+"id": "4c26f2b3928e5c2b",
 "src": "hda",
-"uuid": "cba9b297-4dfe-4063-8510-6c48a1b6b7a1"
+"uuid": "ecb057a2-dbf8-4105-b55e-d726ec1e9693"
 },
 "genbank_files2": {
-"id": "eba7a310b55aafdd",
+"id": "7f1b25c57f1b4097",
 "src": "hda",
-"uuid": "3e8dfce1-7a05-4665-9277-388e3aa42581"
+"uuid": "498fe703-52c3-4162-be00-93f49f00689d"
 },
 "genbank_files3": {
-"id": "eca1089322e0a5fc",
+"id": "cbd9b7f3981a10ff",
 "src": "hda",
-"uuid": "a5d093c2-0087-453e-b7d1-d94a7cb664e0"
+"uuid": "d402c2ac-ca2d-46b6-b9d3-989739678de1"
 },
 "genbank_files4": {
-"id": "0b586e83183b9891",
+"id": "8f1ec376bf339086",
 "src": "hda",
-"uuid": "0ec72cc0-2a95-474b-aa77-7a436dad6a9b"
+"uuid": "1124ff36-f61b-4932-adc6-0b6de5a888ae"
 },
 "genbank_files5": {
-"id": "18d15f79e0c5cee5",
+"id": "a91e9fd0ce2e3c53",
 "src": "hda",
-"uuid": "d272199f-2e1b-49e1-a597-5ffa11507e83"
+"uuid": "8fe51091-39c5-4aa6-b0ec-fbc34712e405"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "cf00b67a5455eb5a",
+"id": "c32c50a47ebf8564",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "684e8d7e5eb8731e",
+"id": "2be24ce9bdbc87e1",
 "src": "hda",
-"uuid": "7435335e-896e-47f4-89c7-3a6c2c25f247"
+"uuid": "45ef7ed5-48aa-4286-ac51-3391b593eb7c"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"BASICAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/10 [00:00<?, ?it/s, now=None]\r                                                          \r\rassembly:   0%|          | 0/8 [00:00<?, ?it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 6/8 [00:00<00:00, 50.04it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/10 [00:00<?, ?it/s, now=None]\r                                                          \r\rassembly:   0%|          | 0/8 [00:00<?, ?it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 6/8 [00:00<00:00, 48.97it/s, now=None]\r                                                                 \r",
 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/10 [00:00<?, ?it/s, now=None]\r                                                          \r\rassembly:   0%|          | 0/8 [00:00<?, ?it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 6/8 [00:00<00:00, 50.04it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/10 [00:00<?, ?it/s, now=None]\r                                                          \r\rassembly:   0%|          | 0/8 [00:00<?, ?it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 6/8 [00:00<00:00, 48.97it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:25:33.071688",
+"update_time": "2025-05-26T12:04:01.978111",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 3,
-"time_seconds": 30.88078260421753,
+"time_seconds": 30.717636823654175,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-3"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "8484dc7b019fd65a",
+"id": "5493159c7d57114c",
 "src": "hda"
 },
 "assembly_plan_name": "BioBrickStandardAssembly",
 "genbank_files": {
-"id": "a3780ecc1a00a0d8",
+"id": "5f035ce298b798b0",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/8/e/2/dataset_8e2dcaab-3dd7-48c4-920e-bdffaad39793.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/d/4/2/dataset_d4271a43-8722-4344-9562-00e9a36d07e5.dat,/tmp/tmpc6lic4p9/files/2/4/8/dataset_2484bbfb-d4b0-4c8b-a57f-675625f98753.dat,/tmp/tmpc6lic4p9/files/8/3/f/dataset_83f035f7-25fc-4a59-83b2-d377e3cd59ad.dat,/tmp/tmpc6lic4p9/files/5/a/a/dataset_5aa7b19e-0ad1-43b1-9083-954067ff2010.dat,/tmp/tmpc6lic4p9/files/d/6/4/dataset_d646b71c-5393-4291-bcc5-7d6cbe22f055.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/d/4/2/dataset_d4271a43-8722-4344-9562-00e9a36d07e5.dat:BBa_E0040_GFP.gb,/tmp/tmpc6lic4p9/files/2/4/8/dataset_2484bbfb-d4b0-4c8b-a57f-675625f98753.dat:BBa_J23119_prom.gb,/tmp/tmpc6lic4p9/files/8/3/f/dataset_83f035f7-25fc-4a59-83b2-d377e3cd59ad.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpc6lic4p9/files/5/a/a/dataset_5aa7b19e-0ad1-43b1-9083-954067ff2010.dat:BBa_J61048_term.gb,/tmp/tmpc6lic4p9/files/d/6/4/dataset_d646b71c-5393-4291-bcc5-7d6cbe22f055.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/35/outputs/dataset_8086c8c0-24b8-4a51-84db-6b4c9b0e76d0.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/4/9/a/dataset_49af2c08-3ad4-4940-ae84-f93df3c0dd8a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat:BBa_E0040_GFP.gb,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat:BBa_J23119_prom.gb,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat:BBa_J61048_term.gb,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/35/outputs/dataset_3f72ea64-02f3-413e-9d9a-5c43eaaadf14.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:25:53.885012",
+"create_time": "2025-05-26T12:04:23.734013",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "153816",
+"external_id": "174889",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "c7c3cd49f3337c1a",
+"history_id": "3937d5ff7c0e1373",
-"id": "684e8d7e5eb8731e",
+"id": "2be24ce9bdbc87e1",
 "inputs": {
 "assembly_csv": {
-"id": "8484dc7b019fd65a",
+"id": "5493159c7d57114c",
 "src": "hda",
-"uuid": "8e2dcaab-3dd7-48c4-920e-bdffaad39793"
+"uuid": "49af2c08-3ad4-4940-ae84-f93df3c0dd8a"
 },
 "genbank_files1": {
-"id": "f007b0e97c7852a9",
+"id": "8d7d89366ae6734b",
 "src": "hda",
-"uuid": "d4271a43-8722-4344-9562-00e9a36d07e5"
+"uuid": "894d0a5e-2d87-4861-85cb-b5cae83b19cb"
 },
 "genbank_files2": {
-"id": "0776247cf19fcdeb",
+"id": "30133c2583e745a4",
 "src": "hda",
-"uuid": "2484bbfb-d4b0-4c8b-a57f-675625f98753"
+"uuid": "315f1808-e9c5-45fb-8cb8-b71e8e1c8366"
 },
 "genbank_files3": {
-"id": "428c69cf899eb78e",
+"id": "d3fd00b679818750",
 "src": "hda",
-"uuid": "83f035f7-25fc-4a59-83b2-d377e3cd59ad"
+"uuid": "b67a6264-6208-4b44-8fd4-47ba3f96faee"
 },
 "genbank_files4": {
-"id": "6576e427b69a444e",
+"id": "a5593c3e02c9d8f6",
 "src": "hda",
-"uuid": "5aa7b19e-0ad1-43b1-9083-954067ff2010"
+"uuid": "ce3a0b5e-0344-4422-b84a-84904818396b"
 },
 "genbank_files5": {
-"id": "bd5ff021b11f5160",
+"id": "fb42640a8a596816",
 "src": "hda",
-"uuid": "d646b71c-5393-4291-bcc5-7d6cbe22f055"
+"uuid": "b7dcace3-2dbd-49db-94ac-98485bf522aa"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "cf75f655bb15877b",
+"id": "fbec4a551130f847",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|C1_prom_barcode__": {
-"id": "db302e29238adc09",
+"id": "f1bdbab1d80457ac",
 "src": "hda",
-"uuid": "d9b71247-a39f-49ea-b279-18a95173730d"
+"uuid": "8a7dec58-9e11-4bbf-a945-3910d02c89d9"
 },
 "__new_primary_file_construct_gb|C2_gfp_term__": {
-"id": "a0c89ee18eccf84a",
+"id": "588795470b41a739",
 "src": "hda",
-"uuid": "cf4710c7-cf67-4f0e-a486-606e525f5689"
+"uuid": "ee52fe89-63a0-498c-bdbb-ec9fe5b72eca"
 },
 "__new_primary_file_construct_gb|C3_final__": {
-"id": "b326684e3f9ff9a4",
+"id": "de619fffe043835f",
 "src": "hda",
-"uuid": "a4ed1a6f-9385-45da-9eda-3fae86d46b5b"
+"uuid": "6b8fe4a1-1743-4ec5-a12e-6b7b267efa08"
 },
 "output_zip": {
-"id": "e3a5c74dec901fc5",
+"id": "a072914da4208f87",
 "src": "hda",
-"uuid": "8086c8c0-24b8-4a51-84db-6b4c9b0e76d0"
+"uuid": "3f72ea64-02f3-413e-9d9a-5c43eaaadf14"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\rassembly:  67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b   | 2/3 [00:00<00:00,  2.10it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.72it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\rassembly:  67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b   | 2/3 [00:00<00:00,  2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.66it/s, now=None]\r                                                                 \r",
 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\rassembly:  67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b   | 2/3 [00:00<00:00,  2.10it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.72it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/3 [00:00<?, ?it/s, now=None]\rassembly:  67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b   | 2/3 [00:00<00:00,  2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.66it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:26:06.650033",
+"update_time": "2025-05-26T12:04:36.963198",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 4,
-"time_seconds": 33.60218787193298,
+"time_seconds": 34.648075580596924,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-4"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "ffdd8176dffd877d",
+"id": "d61e70858d065388",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "744832bdd7ccd728",
+"id": "5bd8560352cb0b69",
 "src": "hdca"
 },
 "genbank_files": {
-"id": "855b83dd0dec8eab",
+"id": "cb2fe7fb50f38553",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/9/8/e/dataset_98e1b862-2d3e-4164-aecf-56bd464d0f11.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/b/6/6/dataset_b66afa5b-682d-49f8-9753-c78c356ff228.dat,/tmp/tmpc6lic4p9/files/4/6/e/dataset_46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c.dat,/tmp/tmpc6lic4p9/files/8/3/5/dataset_8358e657-0e61-486b-adb4-e886f0f354ba.dat,/tmp/tmpc6lic4p9/files/4/c/f/dataset_4cfbb2dd-c5a5-42fe-889b-da6510422b72.dat,/tmp/tmpc6lic4p9/files/2/8/c/dataset_28c96444-abfb-4173-970e-e895146aef97.dat,/tmp/tmpc6lic4p9/files/f/5/4/dataset_f54c7a16-ac6f-42c2-9b6c-345af3050d83.dat,/tmp/tmpc6lic4p9/files/2/a/3/dataset_2a330eb7-d033-4e75-be7a-4473748a6f2d.dat' --domesticated_seq '/tmp/tmpc6lic4p9/files/6/8/7/dataset_6877c227-2c70-4080-962e-ee1855dd797f.dat,/tmp/tmpc6lic4p9/files/e/2/1/dataset_e212262c-a336-4263-a076-2cd300590ba4.dat,/tmp/tmpc6lic4p9/files/4/1/1/dataset_4112d545-7e37-4a6e-8ca8-7c1b8f90a71e.dat,/tmp/tmpc6lic4p9/files/b/3/1/dataset_b31955ce-ea44-4e3a-86a1-6aebc47be841.dat,/tmp/tmpc6lic4p9/files/d/4/d/dataset_d4d14388-55d3-4aec-810d-aa902028f29f.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/b/6/6/dataset_b66afa5b-682d-49f8-9753-c78c356ff228.dat:part_A.gb,/tmp/tmpc6lic4p9/files/4/6/e/dataset_46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c.dat:part_B.gb,/tmp/tmpc6lic4p9/files/8/3/5/dataset_8358e657-0e61-486b-adb4-e886f0f354ba.dat:part_C.gb,/tmp/tmpc6lic4p9/files/4/c/f/dataset_4cfbb2dd-c5a5-42fe-889b-da6510422b72.dat:part_D.gb,/tmp/tmpc6lic4p9/files/2/8/c/dataset_28c96444-abfb-4173-970e-e895146aef97.dat:part_E.gb,/tmp/tmpc6lic4p9/files/f/5/4/dataset_f54c7a16-ac6f-42c2-9b6c-345af3050d83.dat:part_F.gb,/tmp/tmpc6lic4p9/files/2/a/3/dataset_2a330eb7-d033-4e75-be7a-4473748a6f2d.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpc6lic4p9/files/6/8/7/dataset_6877c227-2c70-4080-962e-ee1855dd797f.dat:part_H.gb,/tmp/tmpc6lic4p9/files/e/2/1/dataset_e212262c-a336-4263-a076-2cd300590ba4.dat:part_I.gb,/tmp/tmpc6lic4p9/files/4/1/1/dataset_4112d545-7e37-4a6e-8ca8-7c1b8f90a71e.dat:part_J.gb,/tmp/tmpc6lic4p9/files/b/3/1/dataset_b31955ce-ea44-4e3a-86a1-6aebc47be841.dat:part_K.gb,/tmp/tmpc6lic4p9/files/d/4/d/dataset_d4d14388-55d3-4aec-810d-aa902028f29f.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/49/outputs/dataset_77f39d12-532c-468b-bcf7-fcc1fdedd34c.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/2/3/dataset_f2390ba6-b891-4c75-b5b4-881fabe15212.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat' --domesticated_seq '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat:part_A.gb,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat:part_B.gb,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat:part_C.gb,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat:part_D.gb,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat:part_E.gb,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat:part_H.gb,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat:part_I.gb,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat:part_J.gb,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat:part_K.gb,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/49/outputs/dataset_b5c1d918-9a86-47ac-9fd0-0d1eeecb3515.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:26:47.030790",
+"create_time": "2025-05-26T12:05:17.468278",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "154908",
+"external_id": "176006",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "51c35891e43131e2",
+"history_id": "473b1992d5f5b84f",
-"id": "0b19a103e85bbfbf",
+"id": "52d2dbb7944a53fc",
 "inputs": {
 "assembly_csv": {
-"id": "ffdd8176dffd877d",
+"id": "d61e70858d065388",
 "src": "hda",
-"uuid": "98e1b862-2d3e-4164-aecf-56bd464d0f11"
+"uuid": "f2390ba6-b891-4c75-b5b4-881fabe15212"
 },
 "domesticated_input1": {
-"id": "96e47893a0f61173",
+"id": "201ce005b4eba284",
 "src": "hda",
-"uuid": "6877c227-2c70-4080-962e-ee1855dd797f"
+"uuid": "b263e11f-1d52-45d4-8679-8bb23668154a"
 },
 "domesticated_input2": {
-"id": "07b1a06cea2f6611",
+"id": "ccacdf94e033958e",
 "src": "hda",
-"uuid": "e212262c-a336-4263-a076-2cd300590ba4"
+"uuid": "c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee"
 },
 "domesticated_input3": {
-"id": "7c42ebb9622f8a60",
+"id": "71f633fb8d250097",
 "src": "hda",
-"uuid": "4112d545-7e37-4a6e-8ca8-7c1b8f90a71e"
+"uuid": "ddcb9f93-9b4f-41e3-a1df-5537b6326a78"
 },
 "domesticated_input4": {
-"id": "33456f383510d381",
+"id": "23971c9dcf22198b",
 "src": "hda",
-"uuid": "b31955ce-ea44-4e3a-86a1-6aebc47be841"
+"uuid": "99bac98d-1cbf-4ab1-a680-49cdb721e447"
 },
 "domesticated_input5": {
-"id": "3c2a17e7ec6c065d",
+"id": "60438d790668bc40",
 "src": "hda",
-"uuid": "d4d14388-55d3-4aec-810d-aa902028f29f"
+"uuid": "685cd571-80b5-4c03-b247-4fb51e199639"
 },
 "genbank_files1": {
-"id": "c2ddc784389f17d2",
+"id": "562cdacb0f854350",
 "src": "hda",
-"uuid": "b66afa5b-682d-49f8-9753-c78c356ff228"
+"uuid": "dfe71b71-2603-48cf-bf59-772724abea0f"
 },
 "genbank_files2": {
-"id": "79b5ff6df7bc6716",
+"id": "b5f666ac47f1f830",
 "src": "hda",
-"uuid": "46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c"
+"uuid": "09260017-ac9e-4868-b386-27ef07ca03a8"
 },
 "genbank_files3": {
-"id": "6f172ec7c3220722",
+"id": "316b2bf479d3691f",
 "src": "hda",
-"uuid": "8358e657-0e61-486b-adb4-e886f0f354ba"
+"uuid": "84e57026-4e85-4a63-b66a-8bae5b767f0c"
 },
 "genbank_files4": {
-"id": "0b19a103e85bbfbf",
+"id": "52d2dbb7944a53fc",
 "src": "hda",
-"uuid": "4cfbb2dd-c5a5-42fe-889b-da6510422b72"
+"uuid": "7d26d36d-bb1c-4f83-be4f-3311e4ec2441"
 },
 "genbank_files5": {
-"id": "00fa99289b8a441d",
+"id": "6d0420a098f813ba",
 "src": "hda",
-"uuid": "28c96444-abfb-4173-970e-e895146aef97"
+"uuid": "8a0ff1e5-aaf7-461e-b642-b60e5cf13132"
 },
 "genbank_files6": {
-"id": "95a08e54dcf8e4b4",
+"id": "98086fd4fda4fb74",
 "src": "hda",
-"uuid": "f54c7a16-ac6f-42c2-9b6c-345af3050d83"
+"uuid": "f94fb7c9-761b-4dc1-8caa-a02ee7892c59"
 },
 "genbank_files7": {
-"id": "46fceb9ab6cb9139",
+"id": "1e3f8509b9833e4e",
 "src": "hda",
-"uuid": "2a330eb7-d033-4e75-be7a-4473748a6f2d"
+"uuid": "c7e408b5-927b-4966-8d1f-08de3b41fc34"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "c173cff58a987f8f",
+"id": "1e8e6749bc68d8e8",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "887639ccacb877d4",
+"id": "825e5e92a55932c1",
 "src": "hda",
-"uuid": "ac0f5082-55fc-4fb6-b3ef-f2587cdd2662"
+"uuid": "fd97fd7a-08b9-42ba-ae2a-022c8be1b219"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "97c509c62c06ea77",
+"id": "4a8ace5529c8c3e9",
 "src": "hda",
-"uuid": "9e439105-9563-450d-96a3-bec58242389e"
+"uuid": "b9201d86-ee66-45ac-99a5-09d3ca161d8b"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "05372c5ab71bbd4d",
+"id": "f0d76a7bda3035c9",
 "src": "hda",
-"uuid": "13079e9f-8185-4b43-898a-83348a3fe55b"
+"uuid": "7c74cbab-8a62-43a2-95f3-00919cc11fa7"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "14e667eccbf3c9ac",
+"id": "640790f555d03105",
 "src": "hda",
-"uuid": "4aec2395-19a8-49b5-a927-39b5b06dabe7"
+"uuid": "a450e128-38e8-4eb5-82a1-304b04c68510"
 },
 "output_zip": {
-"id": "edb47c5501e52d48",
+"id": "50943f113f3eedaf",
 "src": "hda",
-"uuid": "77f39d12-532c-468b-bcf7-fcc1fdedd34c"
+"uuid": "b5c1d918-9a86-47ac-9fd0-0d1eeecb3515"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}",
 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.31it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.14it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.74it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.40it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.31it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.14it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.74it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.40it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:27:00.365017",
+"update_time": "2025-05-26T12:05:29.989306",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 5,
-"time_seconds": 53.75153422355652,
+"time_seconds": 53.09692740440369,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-5"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "59a0a00f5fa501d5",
+"id": "d71403ee85b47d8d",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "c9445e550eef23d0",
+"id": "a36db940f4513bd9",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/9/5/0/dataset_9504897d-0d99-44a4-9033-7d14e3943ec9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/a/c/d/dataset_acd9e546-bb31-4391-b867-1d81cab10920.dat,/tmp/tmpc6lic4p9/files/c/f/e/dataset_cfe852f6-5b32-46fd-a9d8-2b777016d403.dat,/tmp/tmpc6lic4p9/files/2/5/b/dataset_25be2770-f768-4b0e-be96-459e47e6ae8d.dat,/tmp/tmpc6lic4p9/files/e/5/8/dataset_e580f806-e8ba-4dac-b8d5-6b76b4a7421b.dat,/tmp/tmpc6lic4p9/files/0/d/6/dataset_0d6de31a-aab1-427f-a2a1-7c8bc988208e.dat,/tmp/tmpc6lic4p9/files/1/2/7/dataset_1272b23f-7cef-4deb-bf92-fbad973bf2c6.dat,/tmp/tmpc6lic4p9/files/7/4/7/dataset_7476b10d-c143-4be7-adb5-118dcf372287.dat,/tmp/tmpc6lic4p9/files/e/2/e/dataset_e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a.dat,/tmp/tmpc6lic4p9/files/c/a/1/dataset_ca18b50c-3b4c-4201-88b0-dffd049718f8.dat,/tmp/tmpc6lic4p9/files/1/b/4/dataset_1b480e84-03cf-4483-9e9e-ccf79bf654a1.dat,/tmp/tmpc6lic4p9/files/b/e/8/dataset_be83b8f4-73de-4775-abb8-75483d4e8ab2.dat,/tmp/tmpc6lic4p9/files/5/d/d/dataset_5ddde548-4828-4067-93b7-1377a71221d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/a/c/d/dataset_acd9e546-bb31-4391-b867-1d81cab10920.dat:part_A.gb,/tmp/tmpc6lic4p9/files/c/f/e/dataset_cfe852f6-5b32-46fd-a9d8-2b777016d403.dat:part_B.gb,/tmp/tmpc6lic4p9/files/2/5/b/dataset_25be2770-f768-4b0e-be96-459e47e6ae8d.dat:part_C.gb,/tmp/tmpc6lic4p9/files/e/5/8/dataset_e580f806-e8ba-4dac-b8d5-6b76b4a7421b.dat:part_D.gb,/tmp/tmpc6lic4p9/files/0/d/6/dataset_0d6de31a-aab1-427f-a2a1-7c8bc988208e.dat:part_E.gb,/tmp/tmpc6lic4p9/files/1/2/7/dataset_1272b23f-7cef-4deb-bf92-fbad973bf2c6.dat:part_F.gb,/tmp/tmpc6lic4p9/files/7/4/7/dataset_7476b10d-c143-4be7-adb5-118dcf372287.dat:part_G.gb,/tmp/tmpc6lic4p9/files/e/2/e/dataset_e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a.dat:part_H.gb,/tmp/tmpc6lic4p9/files/c/a/1/dataset_ca18b50c-3b4c-4201-88b0-dffd049718f8.dat:part_I.gb,/tmp/tmpc6lic4p9/files/1/b/4/dataset_1b480e84-03cf-4483-9e9e-ccf79bf654a1.dat:part_J.gb,/tmp/tmpc6lic4p9/files/b/e/8/dataset_be83b8f4-73de-4775-abb8-75483d4e8ab2.dat:part_K.gb,/tmp/tmpc6lic4p9/files/5/d/d/dataset_5ddde548-4828-4067-93b7-1377a71221d7.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpc6lic4p9/job_working_directory/000/63/outputs/dataset_e10784a6-3050-4131-a684-3847397c4c4d.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/3/c/1/dataset_3c1221bc-ba53-4ede-899c-e4defbe838eb.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat:part_A.gb,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat:part_B.gb,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat:part_C.gb,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat:part_D.gb,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat:part_E.gb,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat:part_F.gb,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat:part_G.gb,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat:part_H.gb,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat:part_I.gb,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat:part_J.gb,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat:part_K.gb,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmpm1fyob3t/job_working_directory/000/63/outputs/dataset_02e7ea5e-6c8f-419d-82de-476bccc550ec.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T11:27:41.184534",
+"create_time": "2025-05-26T12:06:09.749817",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "155964",
+"external_id": "177047",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "84db48b219855f4d",
+"history_id": "9b5c1fe7a52a75e0",
-"id": "14e667eccbf3c9ac",
+"id": "640790f555d03105",
 "inputs": {
 "assembly_csv": {
-"id": "59a0a00f5fa501d5",
+"id": "d71403ee85b47d8d",
 "src": "hda",
-"uuid": "9504897d-0d99-44a4-9033-7d14e3943ec9"
+"uuid": "3c1221bc-ba53-4ede-899c-e4defbe838eb"
 },
 "domesticated_input1": {
-"id": "2252f6534dc04be9",
+"id": "740094ed962e7335",
 "src": "hda",
-"uuid": "acd9e546-bb31-4391-b867-1d81cab10920"
+"uuid": "68ee2e69-c2d9-43cd-851e-0b660884cac2"
 },
 "domesticated_input10": {
-"id": "b26f1eae65161bae",
+"id": "06981e06b6149081",
 "src": "hda",
-"uuid": "1b480e84-03cf-4483-9e9e-ccf79bf654a1"
+"uuid": "04bcf9c1-ccc8-4d52-a739-fb3630f90b05"
 },
 "domesticated_input11": {
-"id": "748ef145f2d110fe",
+"id": "343d33e0d7549cb9",
 "src": "hda",
-"uuid": "be83b8f4-73de-4775-abb8-75483d4e8ab2"
+"uuid": "402aaabe-0ea9-4519-998b-11cf6b07a1df"
 },
 "domesticated_input12": {
-"id": "37a05bd56b325e88",
+"id": "2c330e522704b0f9",
 "src": "hda",
-"uuid": "5ddde548-4828-4067-93b7-1377a71221d7"
+"uuid": "9cf71985-a62d-4d89-845c-2b996d8096fa"
 },
 "domesticated_input2": {
-"id": "2441550d408330ea",
+"id": "839c90adaefe5f3f",
 "src": "hda",
-"uuid": "cfe852f6-5b32-46fd-a9d8-2b777016d403"
+"uuid": "5c298af3-9cdb-4837-8054-8903c2683f85"
 },
 "domesticated_input3": {
-"id": "7982f5ab86225272",
+"id": "1f56aa824e7dde43",
 "src": "hda",
-"uuid": "25be2770-f768-4b0e-be96-459e47e6ae8d"
+"uuid": "9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e"
 },
 "domesticated_input4": {
-"id": "1d0be35bf9fc6600",
+"id": "26b32a65097dcc1d",
 "src": "hda",
-"uuid": "e580f806-e8ba-4dac-b8d5-6b76b4a7421b"
+"uuid": "e77c955d-e9b5-4175-a061-81b9a781d2ff"
 },
 "domesticated_input5": {
-"id": "40fe86a604adcf6d",
+"id": "60327bfb8991788f",
 "src": "hda",
-"uuid": "0d6de31a-aab1-427f-a2a1-7c8bc988208e"
+"uuid": "35df1ceb-416b-4c2d-b20a-3efe96b6770f"
 },
 "domesticated_input6": {
-"id": "7355915c318fd136",
+"id": "ac528058169ea450",
 "src": "hda",
-"uuid": "1272b23f-7cef-4deb-bf92-fbad973bf2c6"
+"uuid": "c02fc9fb-dc4e-49e1-b99f-8199fd97d795"
 },
 "domesticated_input7": {
-"id": "bacbde4487432826",
+"id": "8d7c8aec2b1ab229",
 "src": "hda",
-"uuid": "7476b10d-c143-4be7-adb5-118dcf372287"
+"uuid": "339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a"
 },
 "domesticated_input8": {
-"id": "3b9b440d32d1c6f3",
+"id": "f996cb18f164a451",
 "src": "hda",
-"uuid": "e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a"
+"uuid": "2246947a-dbb7-4ed2-855a-56a42a899aab"
 },
 "domesticated_input9": {
-"id": "a19ae27f3bb8e8c1",
+"id": "f3c4f2ef486441ac",
 "src": "hda",
-"uuid": "ca18b50c-3b4c-4201-88b0-dffd049718f8"
+"uuid": "0a935c03-48a7-4c8a-8077-aea407e5285d"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "fedb85639c7c80b9",
+"id": "182eefa577c2a56d",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "94b6b8378debd859",
+"id": "613a1bff017ef479",
 "src": "hda",
-"uuid": "5145585f-443e-4934-af0b-60e1552a08a9"
+"uuid": "a0c57d2e-8ac7-48d8-b9c5-f01b728ebba7"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "dfa4bbdeadf76cd3",
+"id": "1a8ab2437d7e496f",
 "src": "hda",
-"uuid": "6f0dcaec-2131-4c0c-820b-bb5c895103e2"
+"uuid": "d7804ee2-c9a8-46c2-b057-7f25a8002f55"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "e48032fd92b02fbb",
+"id": "af3c5f81417a677c",
 "src": "hda",
-"uuid": "8c4da7fd-9c6b-4430-9444-c6e89b41c5df"
+"uuid": "71c1f25b-f43d-43f7-9893-bfd3bc967517"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "68bf450f38f03a28",
+"id": "b5b1a9766aab456e",
 "src": "hda",
-"uuid": "a878e0a8-6f34-4cdf-8990-e178d0f15d52"
+"uuid": "f23f1069-e4c4-4a9e-9787-5b2b5e905e24"
 },
 "output_zip": {
-"id": "1062de4bcda0d565",
+"id": "7d40cd3e06526c58",
 "src": "hda",
-"uuid": "e10784a6-3050-4131-a684-3847397c4c4d"
+"uuid": "02e7ea5e-6c8f-419d-82de-476bccc550ec"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
 "genbank_files": null,
 "topology": "\"circular\""
 },
 "state": "ok",
-"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.45it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.84it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.43it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.45it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.84it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.43it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T11:27:53.929264",
+"update_time": "2025-05-26T12:06:22.164674",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fcc5b7d13a1328f6"
+"user_id": "e2ca7f14a85a8d44"
 },
 "status": "success",
 "test_index": 6,
-"time_seconds": 53.42731332778931,
+"time_seconds": 52.117783308029175,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-6"

Mercurial > repos > tduigou > cloning_simulation

comparison output.json @ 15:074a76e84b80 draft